Gentamicin

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Drug Name

Gentamicin is an aminoglycoside used to treat a wide variety of infections caused by gram-positive and gram-negative bacteria, and it is especially effective against severe infections caused by Pseudomonas aeruginosa. Although gentamicin is well-established and may be used in a variety of clinical applications, it is also associated with severe adverse effects, which limits its use. Gentamicin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and impeding the bacteria's ability to synthesize vital proteins.

Table 1. Basic profile of gentamicin.

Description Broad-spectrum aminoglycoside antibiotic
Target(s) Ribosome (30S subunit)
Generic Gentamicin
Commercial Name Gentak, Pred-G, Valisone-G
Combination Drug(s) N/A
Other Synonyms Uromycine, Gentocin, Gentamycinum, Cidomycin, Gentamicins, Gentacycol, Gentavet, Garamycin, Refobacin
IUPAC Name 2-{[4,6-diamino-3-({3-amino-6-[1-(methylamino)ethyl]oxan-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol
Ligand Code in PDB 51G, LLL (bound form)
PDB Structure 4v53 (Escherichia coli ribosome from in complex with gentamicin)
ATC code J01GB03
RotateHydrogensLabels
Figure 1. 2D and 3D structures of Gentamicin (PDB ligand code: LLL).

Antibiotic Chemistry

Gentamicin is made of three rings - a central deoxystreptamine core linked to two amine containing rings purpurosamine and garosamine (Maehr and Schaffner, 1970). This is a highly polar molecule that allows the drug to interact with key residues in the active site.

Figure 2. 2D Chemical structure of gentamicin showing its 3 component rings. Structure created using ChemAxon.
Figure 2. 2D Chemical structure of gentamicin showing its 3 component rings. Structure created using ChemAxon.

Drug Information

Table 2. Chemical and physical properties (DrugBank).

Chemical Formula C21H43N5O7
Molecular Weight 477.595 g/mol
Calculated Predicted Partition Coefficient: cLogP -1.6
Calculated Predicted Aqueous Solubility: cLogS -1.6
Solubility (in water) 12.6 mg/mL
Predicted Topological Polar Surface Area (TPSA) 199.73 Å2

Drug Target

The ribosome is the macromolecular machine on which proteins are synthesized. It is targeted by many classes of antibiotics approved by the US FDA, including aminoglycosides. Gentamicin positions itself in the decoding center of the 30S ribosomal subunit and makes direct contact with rRNA. It directly interferes with the mRNA decoding process in the A-site and as a result, impairs the ribosome’s ability to insert the correct amino acids into nascent polypeptide chains. In addition, the antibiotic may also bind to other sites on the ribosome interfering with ribosome recycling (Borovinskaya et al., 2007).

Learn more about protein synthesis and the ribosome here.

Drug-Target Complex

The E. coli ribosome (shown in Figure 3) consists of the 50S subunit and the 30s subunit. Gentamicin binds at multiple sites on the 30S and even at the interface between the 30s and 50S subunits (Figure 3, left). The primary binding site is still near the A-site, where it interacts via hydrogen binds with bases A1408, G1494, U1495, and G1405 (Figure 3 right, top panel). As a result of gentamicin binding, incorrect amino acids are inserted into nascent polypeptide chains during translation, producing nonfunctional proteins.

Additionally, the structure shows that gentamycin also binds to a few other locations at a lower occupancy. Binding at one of these locations is shown, where gentamicin interacts via hydrogen bonds with nucleotides C1920–C1925 and G1906 (Figure 3, right, bottom panel). These interactions may have a role in gentamicin's role in ribosome recycling (Borovinskaya et al., 2007).

Figure 3. The binding site of gentamicin and the major interactions of the drug with the ribosome (PDB ID: 4v53, Borovinskaya et al., 2007).
Figure 3. The binding site of gentamicin and the major interactions of the drug with the ribosome (PDB ID: 4v53, Borovinskaya et al., 2007).

Pharmacologic Properties and Safety

Table 3. Pharmacokinetics: ADMET of gentamicin.

Features Comment(s) Source
Oral Bioavailability (%) 0 DrugBank
IC50 0.5 mg/L (Cha, 2008)
Ki (μM) N/A N/A
Half-Life (hrs) 1.25 - 1.75 hours DrugBank
Duration of Action 8-12 hours FDA
Absorption Site N/A N/A
Transporter(s) N/A N/A
Metabolism Gentamicin undergoes little to no metabolism DrugBank
Excretion ~ 70% of gentamicin is recovered in the urine within 24 hours DrugBank
AMES Test (Carcinogenic Effect) Probability 0.7338 (Non-AMES toxic) DrugBank
hERG Safety Test (Cardiac Effect) Probability 0.9696 (Non-carcinogen) DrugBank
Liver Toxicity Aminoglycosides are not listed or mentioned in large case series of drug-induced liver disease and acute liver failure; thus, hepatic injury due to gentamicin is rare. LiverTox

Drug Interactions and Side Effects

Table 4. Drug interactions and side effects of gentamicin.

Features Comment(s) Source
Total Number of Drug Interactions 174 drugs Drugs.com
Major Drug Interactions 61 major drug interactions Drugs.com
Alcohol/Food Interactions N/A N/A
Disease Interactions Dehydration (major) Neuromuscular blockage (major) Ototoxicity (major) Renal dysfunction (major) Drugs.com
On-Target Side Effects Pain at injection site Drugs.com
Off-Target Side Effects Vision problems; nausea, vomiting, loss of appetite, weight loss; a light-headed feeling, like you might pass out; itching or rash; pain where the medicine was injected; headache, mood changes; or joint pain Drugs.com
CYP Interactions CYP450 3A4 substrate DrugBank

Links

Table 5. Links to learn more about gentamicin.

Comprehensive Antibiotic Resistance Database (CARD) ARO:0000014
DrugBank DB00798
Drugs.com https://www.drugs.com/mtm/gentamicin.html
FDA – Gentamicin Injection https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/062366s033lbl.pdf
LiverTox: National Institutes of Health (NIH) https://www.ncbi.nlm.nih.gov/books/NBK548706/
PubChem CID 3467

Learn about gentamycin resistance.

References

Borovinskaya, M. A., Pai, R. D., Zhang, W., Schuwirth, B. S., Holton, J. M., Hirokawa, G., Kaji, H., Kaji, A., Cate, J. H. (2007). Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nature structural & molecular biology, 14(8), 727-732. https://doi.org/10.1038/nsmb1271

Cha, R. (2008). In Vitro Activity of Cefepime, Imipenem, Tigecycline, and Gentamicin, Alone and in Combination, Against Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae and Escherichia coli. Pharmacotherapy, 28(3), 295–300. https://doi.org/10.1592/phco.28.3.295

Gentamicin – DrugBank. Drugbank.ca. https://go.drugbank.com/drugs/DB00798

Gentamicin. Drugs.com. https://www.drugs.com/mtm/gentamicin.html

Gentamicin. PubChem. https://pubchem.ncbi.nlm.nih.gov/compound/Gentamicin

Gentamicin Injection. Food and Drug Administration. https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/062366s033lbl.pdf

Jia, B., Raphenya, A. R., Alcock, B., Waglechner, N., Guo, P., Tsang, K. K., Lago, B. A., Dave, B. M., Pereira, S., Sharma, A. N., Doshi, S., Courtot, M., Lo, R., Williams, L. E., Frye, J. G., Elsayegh, T., Sardar, D. Westman, E. L., Pawlowski, A. C., Johnson, T. A., Brinkman, F. S., Wright, G. D., and McArthur, A. G. (2017) CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research 45, D566-573. https://doi.org/10.1093/nar/gkw1004

LiverTox – Clinical and Research Information on Drug-Induced Liver Injury. National Institutes of Health. https://www.ncbi.nlm.nih.gov/books/NBK548706/

Maehr, H., Schaffner, C. P. (1970) Chemistry of the gentamicins. II. Stereochemistry and synthesis of gentosamine. Total structure of gentamicin A. J Am Chem Soc. 92(6):1697-700. https://doi.org/10.1021/ja00709a047

March 2025, Helen Gao, Shuchismita Dutta; Reviewed by Drs. Albert Berghuis and Tolou Golkar
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/prot-syn/ribo/AMG/gentamicin